Vaccines in the pipeline

Circle packing

Photo by CDC on Unsplash

Swine Flu vaccination administered by way of a jet injector known as a “Ped-O-Jet®”, 1976

Science is telling us that we can do phenomenal things if we put our minds and our resources to it…
— Anthony Fauci

To facilitate the creation and dissemination of new vaccines, the WHO maintains a list of vaccines in the “pipeline” for clinical trials. The sources on information for these trials are clinicaltrials.gov and who.int/ictrp, which includes clinical trial registries from 17 countries. Some information is also obtained through contact with investigators, sponsors, and funders of vaccine trials.

Ingest the data

disease, phases, and sample size enrollment

df_file_path <- "archetypes/vaccines-in-the-pipeline/new-vaccines-in-the-pipeline.csv"
df = read.csv(df_file_path, header = TRUE, stringsAsFactors = FALSE)
df

Wrangle the data

Create node and edge tables

# Complete cases
df_wrangle <- df %>% mutate(ID = row_number(), Size = as.numeric(Sample.Size..Enrollment))
df_wrangle <- filter(df_wrangle, Size > 0 )
df_wrangle <- filter(df_wrangle, nchar(Registry.ID) > 0 )

# Unique edges
df_edges <- aggregate(x = df_wrangle$Size,
          by = list(df_wrangle$Disease, df_wrangle$Registry.ID),
          FUN = sum)

# Standard edge table structure
colnames(df_edges) <- c("FROM","TO", "SIZE")

# Root nodes
df_nodes_1 <- aggregate(x = df_wrangle$Size,
          by = list(df_wrangle$Disease),
          FUN = sum)

colnames(df_nodes_1) <- c("NODE","SIZE")
df_nodes_1$COLOR <- "0"

# Leaf nodes
df_nodes_2 <- df_wrangle %>% select(Registry.ID, PNUM, Size)
colnames(df_nodes_2) <- c("NODE", "COLOR", "SIZE")

# Combine
df_nodes <- rbind(df_nodes_1, df_nodes_2)

# Complete cases
df_nodes <- filter(df_nodes, SIZE > 0 )


# Transform to graph data structure
df_graph <- graph_from_data_frame( df_edges, vertices = df_nodes )

edge table

df_edges

node table

df_nodes

Plot

circle pack layout with size, color, and labels (at root level)

theme_opts <- theme(
    text = element_text(family = "inconsolata"), 
    legend.position='none'
  )

phase_pal <- c("0" = "#FFFFFF", "1" = "#6A1B9A", "1.5" = "#7B1FA2", "2" = "#8E24AA",
               "2.5" = "#9C27B0", "3" = "#AB47BC", "3.5" = "#BA68C8", "4" = "#CE93D8")

v1 <- ggraph(df_graph, layout = 'circlepack', weight = SIZE) + 
  geom_node_circle(aes(fill = COLOR)) + 
  scale_fill_manual(values = phase_pal) +
  geom_node_label( aes(label=name, filter=depth==0), size = 6, family = "inconsolata") +
  coord_fixed() + 
  theme_void() +
  theme_opts

girafe(ggobj = v1, width_svg = 1280/72, height_svg = 720/72,
       options = list(opts_sizing(rescale = TRUE, width = 1.0))
)

References

citations for narrative and data sources

Narrative sources
Data sources: WHO vaccine pipeline tracker, World Health Organization, http://www.who.int/immunization/research/vaccine_pipeline_tracker_spreadsheet/en/